File size: 3,547 Bytes
3799002 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 | """Inspect extra_tooth_labels/ and report which case each file maps to + what
preprocess.assemble_label will do.
python -m toothcanal.inspect_labels --config configs/default.yaml
Use this BEFORE running preprocess on cases 21-30: it tells you which files in
extra_tooth_labels/ are recognized, which case each is mapped to, and whether
the content already contains tooth bodies (overrides HF label) or only teeth /
only canal (needs merging).
"""
import os, re, glob, argparse
import numpy as np
from .utils import load_config, load_nii
def case_candidates(name):
"""Return the set of plausible case numbers (1..40) suggested by filename."""
import re
runs = re.findall(r"\d+", name)
plausible = set()
for r in runs:
n = int(r)
if 1 <= n <= 40:
plausible.add(n)
for w in (2, 3):
for i in range(len(r) - w + 1):
n = int(r[i:i + w])
if 1 <= n <= 40:
plausible.add(n)
return sorted(plausible)
def main():
ap = argparse.ArgumentParser()
ap.add_argument("--config", default="configs/default.yaml")
args = ap.parse_args()
cfg = load_config(args.config)
extra = cfg["paths"].get("extra_tooth_dir")
if not extra or not os.path.isdir(extra):
raise SystemExit(f"extra_tooth_dir not found: {extra}")
ls = cfg["label_scheme"]
cands = sorted(glob.glob(os.path.join(extra, "**", "*.nii.gz"), recursive=True))
if not cands:
raise SystemExit(f"no .nii.gz files in {extra}")
print(f"\nInspecting {len(cands)} files in {extra}\n")
print(f"{'file':50s} {'cases':>14s} {'shape':>15s} {'labels':>40s} verdict")
print("-" * 145)
by_case = {}
for p in cands:
base = os.path.basename(p)
guesses = case_candidates(base)
try:
vol, _ = load_nii(p)
vol = np.rint(vol).astype(np.int16)
uniq = sorted(int(v) for v in np.unique(vol) if v != 0)
except Exception as e:
print(f"{base:50s} READ FAIL: {e}")
continue
has_canal = any(ls["canal_lo"] <= v <= ls["canal_hi"] for v in uniq)
has_body = any(ls["body_lo"] <= v <= ls["body_hi"] for v in uniq)
if has_canal and has_body:
verdict = "COMPLETE (will override HF label)"
elif has_canal and not has_body:
verdict = "canal-only (won't be used; rename / replace)"
elif has_body and not has_canal:
verdict = "body-only (will be merged with HF canal)"
else:
verdict = "binary or unknown -> will be merged"
head = (str(uniq)[:38] + "..") if len(str(uniq)) > 40 else str(uniq)
cstr = ",".join(str(c) for c in guesses) if guesses else "-"
print(f"{base[:50]:50s} {cstr:>14s} {str(vol.shape):>15s} {head:>40s} {verdict}")
for n in guesses:
by_case.setdefault(n, []).append((base, verdict))
print("\nPer-case summary (production resolution via find_extra_tooth):")
from .assemble import find_extra_tooth
extra_dir = cfg["paths"]["extra_tooth_dir"]
chosen = {}
for n in range(1, 41):
p = find_extra_tooth(n, extra_dir)
if p:
chosen[n] = os.path.basename(p)
for n in sorted(chosen):
print(f" case {n:>2}: -> {chosen[n]}")
missing = [n for n in range(21, 31) if n not in chosen]
if missing:
print(f"\n WARNING: no extra label resolved for cases {missing} in 21-30 range.")
if __name__ == "__main__":
main()
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